Re: UmlsUserApprover Error [EXTERNAL]
Hi Sean and everybody, I just wanted to confirm that I intermittently run into the same issue. I was able to fix it yesterday by removing a bunch of files from /tmp (such as conn.xml, which dictionary lookup apparently creates there under my user name). However, today, the problem returned and I haven’t found a way to fix it. Again, the same pipeline runs fine on my laptop (Mac OS) and another machine that runs Linux. Dima On Mar 13, 2018, at 14:13, Andrew Phillips <aphilli...@luc.edu<mailto:aphilli...@luc.edu>> wrote: Hi Sean, I looked into changing the relevant configs to non-checking, but didn't have much success. I am back to primarily trying to troubleshoot the original error. I have tried removing files from /tmp (especially conn.xml) as they seemed to be contributing to the issue. I also tried setting up cTAKES with a freshly created account, and am still encountering this issue. Other users on the server also have varying mileage with the same task. Do you have any more ideas of anything else I can try? Thank you. *Andrew Phillips* GitHub: github.com/skeledrew<http://github.com/skeledrew> LinkedIn: www.linkedin.com/in/aphillipstech<http://www.linkedin.com/in/aphillipstech> On 27 February 2018 at 17:45, Finan, Sean <sean.fi...@childrens.harvard.edu<mailto:sean.fi...@childrens.harvard.edu>> wrote: Hi Andrew, If you created your own dictionary then you are already bound by your own license credentials used to get the umls download. You do not need to use the ctakes license check. In your lookup configuration xml file you can change the UmlsJdbc** to the non-checking Jdbc**. There are several email threads with associated information such as http://mail-archives.apache.org/mod_mbox/ctakes-dev/ 201802.mbox/%3CCANLSW%2B%3DbGXkqDoY_fUMc%3DgvGjLbTfXfL4aq7vy-abe% 3DW6qm6Vw%40mail.gmail.com<http://40mail.gmail.com>%3E Sean -Original Message- From: Andrew Phillips [mailto:aphilli...@luc.edu] Sent: Tuesday, February 27, 2018 5:13 PM To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subject: Re: UmlsUserApprover Error [EXTERNAL] Hi Sean, I am using a dictionary created from the 2017AA-full which I downloaded from the UTS site. Does this count as default? *Andrew Phillips* GitHub: github.com/skeledrew<http://github.com/skeledrew> LinkedIn: www.linkedin.com/in/aphillipstech<http://www.linkedin.com/in/aphillipstech> On 27 February 2018 at 15:41, Finan, Sean <Sean.Finan@childrens.harvard<mailto:Sean.Finan@childrens.harvard>. edu> wrote: Hi Andrew, As far as I know there isn't an explicit timeout imposed by ctakes. There is probably a java or system timeout, but I don't know of an easy way to change it. If you use the default dictionary then you should allow the account check. Sean -Original Message- From: Andrew Phillips [mailto:aphilli...@luc.edu] Sent: Tuesday, February 27, 2018 4:27 PM To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subject: Re: UmlsUserApprover Error [EXTERNAL] @Gandhi: I have always skipped the tests whenever I run the install command. @Sean: 2 of the 4 folders I ran on were eventually processed, and only after running the script multiple times, so it does seem to be a connection issue. However I am trying to run the commands for the last couple of folders manually and the error has been consistent. Is there any way to bypass the account check, or increase the timeout? Or can I just have a loop that continually retries until the operation succeeds? *Andrew Phillips* GitHub: github.com/skeledrew<http://github.com/skeledrew> LinkedIn: www.linkedin.com/in/aphillipstech<http://www.linkedin.com/in/aphillipstech> On 27 February 2018 at 07:18, Finan, Sean <Sean.Finan@childrens.harvard<mailto:Sean.Finan@childrens.harvard>. edu> wrote: Hi Andrew, You wrote: I ran my script earlier, [...]and only the first run was successful. Are you saying that one run did succeed? If that is the case then the problem probably is your network. The umls credential check will print dots in the log as time progresses, such as the dots from your log below: 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS Account [ ... ] .. 10 ... 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov<http://uts-ws.nlm.nih.gov> It looks like the credential check took several (~15?) seconds, which might indicate a slow connection or an eventual connection refused. That does not mean that the slowdown is on your side. It could be that the nih server that handles the credential checks is rarely getting to your request. I'm not sure why that would be (No net neutrality rants, please). Anyway, if the credential check works even once then that is a good indication that the problem is outside ctakes. Sean -Original Message- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@ari
Re: UmlsUserApprover Error [EXTERNAL]
Hi Sean, I looked into changing the relevant configs to non-checking, but didn't have much success. I am back to primarily trying to troubleshoot the original error. I have tried removing files from /tmp (especially conn.xml) as they seemed to be contributing to the issue. I also tried setting up cTAKES with a freshly created account, and am still encountering this issue. Other users on the server also have varying mileage with the same task. Do you have any more ideas of anything else I can try? Thank you. *Andrew Phillips* GitHub: github.com/skeledrew LinkedIn: www.linkedin.com/in/aphillipstech On 27 February 2018 at 17:45, Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > Hi Andrew, > > If you created your own dictionary then you are already bound by your own > license credentials used to get the umls download. You do not need to use > the ctakes license check. > > In your lookup configuration xml file you can change the UmlsJdbc** to the > non-checking Jdbc**. There are several email threads with associated > information such as http://mail-archives.apache.org/mod_mbox/ctakes-dev/ > 201802.mbox/%3CCANLSW%2B%3DbGXkqDoY_fUMc%3DgvGjLbTfXfL4aq7vy-abe% > 3DW6qm6Vw%40mail.gmail.com%3E > > Sean > > -Original Message- > From: Andrew Phillips [mailto:aphilli...@luc.edu] > Sent: Tuesday, February 27, 2018 5:13 PM > To: dev@ctakes.apache.org > Subject: Re: UmlsUserApprover Error [EXTERNAL] > > Hi Sean, > > I am using a dictionary created from the 2017AA-full which I downloaded > from the UTS site. Does this count as default? > > *Andrew Phillips* > GitHub: github.com/skeledrew > LinkedIn: www.linkedin.com/in/aphillipstech > > On 27 February 2018 at 15:41, Finan, Sean <Sean.Finan@childrens.harvard. > edu> > wrote: > > > Hi Andrew, > > > > As far as I know there isn't an explicit timeout imposed by ctakes. > > There is probably a java or system timeout, but I don't know of an > > easy way to change it. > > > > If you use the default dictionary then you should allow the account > check. > > > > Sean > > > > -Original Message- > > From: Andrew Phillips [mailto:aphilli...@luc.edu] > > Sent: Tuesday, February 27, 2018 4:27 PM > > To: dev@ctakes.apache.org > > Subject: Re: UmlsUserApprover Error [EXTERNAL] > > > > @Gandhi: I have always skipped the tests whenever I run the install > > command. > > > > @Sean: 2 of the 4 folders I ran on were eventually processed, and only > > after running the script multiple times, so it does seem to be a > > connection issue. However I am trying to run the commands for the last > > couple of folders manually and the error has been consistent. Is there > > any way to bypass the account check, or increase the timeout? Or can I > > just have a loop that continually retries until the operation succeeds? > > > > *Andrew Phillips* > > GitHub: github.com/skeledrew > > LinkedIn: www.linkedin.com/in/aphillipstech > > > > On 27 February 2018 at 07:18, Finan, Sean <Sean.Finan@childrens.harvard. > > edu> > > wrote: > > > > > Hi Andrew, > > > > > > You wrote: > > > > I ran my script earlier, [...]and only the first run was successful. > > > > > > Are you saying that one run did succeed? If that is the case then > > > the problem probably is your network. > > > > > > The umls credential check will print dots in the log as time > > > progresses, such as the dots from your log below: > > > > > 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS > > > > > Account > > > [ ... ] > > > > > .. 10 ... > > > > > 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov > > > > > > It looks like the credential check took several (~15?) seconds, > > > which might indicate a slow connection or an eventual connection > refused. > > > That does not mean that the slowdown is on your side. It could be > > > that the nih server that handles the credential checks is rarely > > > getting to your request. I'm not sure why that would be (No net > > neutrality rants, please). > > > > > > Anyway, if the credential check works even once then that is a good > > > indication that the problem is outside ctakes. > > > > > > Sean > > > > > > > > > > > > > > > > > > > > > -Original Message- > > > From: Gandhi Rajan Natarajan > > > [mailto:gandhi.natara...@arisglobal.co
RE: UmlsUserApprover Error [EXTERNAL]
Hi Andrew, If you created your own dictionary then you are already bound by your own license credentials used to get the umls download. You do not need to use the ctakes license check. In your lookup configuration xml file you can change the UmlsJdbc** to the non-checking Jdbc**. There are several email threads with associated information such as http://mail-archives.apache.org/mod_mbox/ctakes-dev/201802.mbox/%3CCANLSW%2B%3DbGXkqDoY_fUMc%3DgvGjLbTfXfL4aq7vy-abe%3DW6qm6Vw%40mail.gmail.com%3E Sean -Original Message- From: Andrew Phillips [mailto:aphilli...@luc.edu] Sent: Tuesday, February 27, 2018 5:13 PM To: dev@ctakes.apache.org Subject: Re: UmlsUserApprover Error [EXTERNAL] Hi Sean, I am using a dictionary created from the 2017AA-full which I downloaded from the UTS site. Does this count as default? *Andrew Phillips* GitHub: github.com/skeledrew LinkedIn: www.linkedin.com/in/aphillipstech On 27 February 2018 at 15:41, Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > Hi Andrew, > > As far as I know there isn't an explicit timeout imposed by ctakes. > There is probably a java or system timeout, but I don't know of an > easy way to change it. > > If you use the default dictionary then you should allow the account check. > > Sean > > -Original Message- > From: Andrew Phillips [mailto:aphilli...@luc.edu] > Sent: Tuesday, February 27, 2018 4:27 PM > To: dev@ctakes.apache.org > Subject: Re: UmlsUserApprover Error [EXTERNAL] > > @Gandhi: I have always skipped the tests whenever I run the install > command. > > @Sean: 2 of the 4 folders I ran on were eventually processed, and only > after running the script multiple times, so it does seem to be a > connection issue. However I am trying to run the commands for the last > couple of folders manually and the error has been consistent. Is there > any way to bypass the account check, or increase the timeout? Or can I > just have a loop that continually retries until the operation succeeds? > > *Andrew Phillips* > GitHub: github.com/skeledrew > LinkedIn: www.linkedin.com/in/aphillipstech > > On 27 February 2018 at 07:18, Finan, Sean <Sean.Finan@childrens.harvard. > edu> > wrote: > > > Hi Andrew, > > > > You wrote: > > > I ran my script earlier, [...]and only the first run was successful. > > > > Are you saying that one run did succeed? If that is the case then > > the problem probably is your network. > > > > The umls credential check will print dots in the log as time > > progresses, such as the dots from your log below: > > > > 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS > > > > Account > > [ ... ] > > > > .. 10 ... > > > > 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov > > > > It looks like the credential check took several (~15?) seconds, > > which might indicate a slow connection or an eventual connection refused. > > That does not mean that the slowdown is on your side. It could be > > that the nih server that handles the credential checks is rarely > > getting to your request. I'm not sure why that would be (No net > neutrality rants, please). > > > > Anyway, if the credential check works even once then that is a good > > indication that the problem is outside ctakes. > > > > Sean > > > > > > > > > > > > > > -Original Message- > > From: Gandhi Rajan Natarajan > > [mailto:gandhi.natara...@arisglobal.com] > > Sent: Tuesday, February 27, 2018 7:49 AM > > To: dev@ctakes.apache.org > > Subject: RE: UmlsUserApprover Error [EXTERNAL] > > > > I guess you are running the build with test cases as I see the below > > messages in my case only while running build with test cases: > > > > >> log4j: reset attribute= "false". > > > > log4j: Threshold ="null". > > > > log4j: Retreiving an instance of org.apache.log4j.Logger. > > > > log4j: Setting [ProgressAppender] additivity to [false]. > > > > log4j: Level value for ProgressAppender is [INFO]. > > > > log4j: ProgressAppender level set to INFO > > > > > > Could you try building ' ctakes-temporal' module by skipping test > > case using the command - " mvn clean install -Dmaven.test.skip=true" ? > > > > Regards, > > Gandhi > > > > -Original Message- > > From: Andrew Phillips [mailto:aphilli...@luc.edu] > > Sent: Tuesday, February 27, 2018 7:08 AM > > To: dev@ctakes.apache.org > > Subject: Re: UmlsUser
Re: UmlsUserApprover Error [EXTERNAL]
Hi Sean,
I am using a dictionary created from the 2017AA-full which I downloaded
from the UTS site. Does this count as default?
*Andrew Phillips*
GitHub: github.com/skeledrew
LinkedIn: www.linkedin.com/in/aphillipstech
On 27 February 2018 at 15:41, Finan, Sean <sean.fi...@childrens.harvard.edu>
wrote:
> Hi Andrew,
>
> As far as I know there isn't an explicit timeout imposed by ctakes. There
> is probably a java or system timeout, but I don't know of an easy way to
> change it.
>
> If you use the default dictionary then you should allow the account check.
>
> Sean
>
> -Original Message-
> From: Andrew Phillips [mailto:aphilli...@luc.edu]
> Sent: Tuesday, February 27, 2018 4:27 PM
> To: dev@ctakes.apache.org
> Subject: Re: UmlsUserApprover Error [EXTERNAL]
>
> @Gandhi: I have always skipped the tests whenever I run the install
> command.
>
> @Sean: 2 of the 4 folders I ran on were eventually processed, and only
> after running the script multiple times, so it does seem to be a connection
> issue. However I am trying to run the commands for the last couple of
> folders manually and the error has been consistent. Is there any way to
> bypass the account check, or increase the timeout? Or can I just have a
> loop that continually retries until the operation succeeds?
>
> *Andrew Phillips*
> GitHub: github.com/skeledrew
> LinkedIn: www.linkedin.com/in/aphillipstech
>
> On 27 February 2018 at 07:18, Finan, Sean <Sean.Finan@childrens.harvard.
> edu>
> wrote:
>
> > Hi Andrew,
> >
> > You wrote:
> > > I ran my script earlier, [...]and only the first run was successful.
> >
> > Are you saying that one run did succeed? If that is the case then the
> > problem probably is your network.
> >
> > The umls credential check will print dots in the log as time
> > progresses, such as the dots from your log below:
> > > > 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS
> > > > Account
> > [ ... ]
> > > > .. 10
> > > > ...
> > > > 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov
> >
> > It looks like the credential check took several (~15?) seconds, which
> > might indicate a slow connection or an eventual connection refused.
> > That does not mean that the slowdown is on your side. It could be
> > that the nih server that handles the credential checks is rarely
> > getting to your request. I'm not sure why that would be (No net
> neutrality rants, please).
> >
> > Anyway, if the credential check works even once then that is a good
> > indication that the problem is outside ctakes.
> >
> > Sean
> >
> >
> >
> >
> >
> >
> > -Original Message-
> > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> > Sent: Tuesday, February 27, 2018 7:49 AM
> > To: dev@ctakes.apache.org
> > Subject: RE: UmlsUserApprover Error [EXTERNAL]
> >
> > I guess you are running the build with test cases as I see the below
> > messages in my case only while running build with test cases:
> >
> > >> log4j: reset attribute= "false".
> > > > log4j: Threshold ="null".
> > > > log4j: Retreiving an instance of org.apache.log4j.Logger.
> > > > log4j: Setting [ProgressAppender] additivity to [false].
> > > > log4j: Level value for ProgressAppender is [INFO].
> > > > log4j: ProgressAppender level set to INFO
> >
> >
> > Could you try building ' ctakes-temporal' module by skipping test case
> > using the command - " mvn clean install -Dmaven.test.skip=true" ?
> >
> > Regards,
> > Gandhi
> >
> > -Original Message-
> > From: Andrew Phillips [mailto:aphilli...@luc.edu]
> > Sent: Tuesday, February 27, 2018 7:08 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: UmlsUserApprover Error [EXTERNAL]
> >
> > Thanks for the ideas.
> >
> > There hasn't been any such changes, and network connectivity shouldn't
> > be an issue. I ran my script earlier, which automatically runs the
> > same pipeline on several different folders, and only the first run was
> > successful. The others failed with the same error. My latest attempt
> > is to remove the .m2 directory and recompile and reinstall, and it is
> > currently processing the first directory, so I don't know if it will
> > fail on the next as yet.
> >
> > My primary interface is over SSH to a remote server, and this is the
> > script:
> > UmlsLP () {
RE: UmlsUserApprover Error [EXTERNAL]
Hi Andrew,
As far as I know there isn't an explicit timeout imposed by ctakes. There is
probably a java or system timeout, but I don't know of an easy way to change
it.
If you use the default dictionary then you should allow the account check.
Sean
-Original Message-
From: Andrew Phillips [mailto:aphilli...@luc.edu]
Sent: Tuesday, February 27, 2018 4:27 PM
To: dev@ctakes.apache.org
Subject: Re: UmlsUserApprover Error [EXTERNAL]
@Gandhi: I have always skipped the tests whenever I run the install command.
@Sean: 2 of the 4 folders I ran on were eventually processed, and only after
running the script multiple times, so it does seem to be a connection issue.
However I am trying to run the commands for the last couple of folders manually
and the error has been consistent. Is there any way to bypass the account
check, or increase the timeout? Or can I just have a loop that continually
retries until the operation succeeds?
*Andrew Phillips*
GitHub: github.com/skeledrew
LinkedIn: www.linkedin.com/in/aphillipstech
On 27 February 2018 at 07:18, Finan, Sean <sean.fi...@childrens.harvard.edu>
wrote:
> Hi Andrew,
>
> You wrote:
> > I ran my script earlier, [...]and only the first run was successful.
>
> Are you saying that one run did succeed? If that is the case then the
> problem probably is your network.
>
> The umls credential check will print dots in the log as time
> progresses, such as the dots from your log below:
> > > 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS
> > > Account
> [ ... ]
> > > .. 10
> > > ...
> > > 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov
>
> It looks like the credential check took several (~15?) seconds, which
> might indicate a slow connection or an eventual connection refused.
> That does not mean that the slowdown is on your side. It could be
> that the nih server that handles the credential checks is rarely
> getting to your request. I'm not sure why that would be (No net neutrality
> rants, please).
>
> Anyway, if the credential check works even once then that is a good
> indication that the problem is outside ctakes.
>
> Sean
>
>
>
>
>
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Tuesday, February 27, 2018 7:49 AM
> To: dev@ctakes.apache.org
> Subject: RE: UmlsUserApprover Error [EXTERNAL]
>
> I guess you are running the build with test cases as I see the below
> messages in my case only while running build with test cases:
>
> >> log4j: reset attribute= "false".
> > > log4j: Threshold ="null".
> > > log4j: Retreiving an instance of org.apache.log4j.Logger.
> > > log4j: Setting [ProgressAppender] additivity to [false].
> > > log4j: Level value for ProgressAppender is [INFO].
> > > log4j: ProgressAppender level set to INFO
>
>
> Could you try building ' ctakes-temporal' module by skipping test case
> using the command - " mvn clean install -Dmaven.test.skip=true" ?
>
> Regards,
> Gandhi
>
> -Original Message-
> From: Andrew Phillips [mailto:aphilli...@luc.edu]
> Sent: Tuesday, February 27, 2018 7:08 AM
> To: dev@ctakes.apache.org
> Subject: Re: UmlsUserApprover Error [EXTERNAL]
>
> Thanks for the ideas.
>
> There hasn't been any such changes, and network connectivity shouldn't
> be an issue. I ran my script earlier, which automatically runs the
> same pipeline on several different folders, and only the first run was
> successful. The others failed with the same error. My latest attempt
> is to remove the .m2 directory and recompile and reinstall, and it is
> currently processing the first directory, so I don't know if it will
> fail on the next as yet.
>
> My primary interface is over SSH to a remote server, and this is the
> script:
> UmlsLP () { mvn exec:java
> -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
> -Dexec.args="--input-dir $1/yes/ --output-dir $2/yes/"
> -Dctakes.umlsuser= -Dctakes.umlspw= > out.tmp ; mvn
> exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
> -Dexec.args="--input-dir $1/no/ --output-dir $2/no/"
> -Dctakes.umlsuser= -Dctakes.umlspw= >> out.tmp ; echo
> Finished UmlsLP $1 $2 ; cat out.tmp | grep -C 3 "Total time" ;}
>
> Thank you.
>
>
> *Andrew Phillips*
> GitHub: github.com/skeledrew
> LinkedIn: www.linkedin.com/in/aphillipstech
>
> On 26 February 2018 at 13:00, Miller, Timothy < Timothy.Miller@childrens.
> harvard.edu> wrote:
>
> > Is it possible
Re: UmlsUserApprover Error [EXTERNAL]
@Gandhi: I have always skipped the tests whenever I run the install command.
@Sean: 2 of the 4 folders I ran on were eventually processed, and only
after running the script multiple times, so it does seem to be a connection
issue. However I am trying to run the commands for the last couple of
folders manually and the error has been consistent. Is there any way to
bypass the account check, or increase the timeout? Or can I just have a
loop that continually retries until the operation succeeds?
*Andrew Phillips*
GitHub: github.com/skeledrew
LinkedIn: www.linkedin.com/in/aphillipstech
On 27 February 2018 at 07:18, Finan, Sean <sean.fi...@childrens.harvard.edu>
wrote:
> Hi Andrew,
>
> You wrote:
> > I ran my script earlier, [...]and only the first run was successful.
>
> Are you saying that one run did succeed? If that is the case then the
> problem probably is your network.
>
> The umls credential check will print dots in the log as time progresses,
> such as the dots from your log below:
> > > 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS Account
> [ ... ]
> > > .. 10
> > > ...
> > > 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov
>
> It looks like the credential check took several (~15?) seconds, which
> might indicate a slow connection or an eventual connection refused. That
> does not mean that the slowdown is on your side. It could be that the nih
> server that handles the credential checks is rarely getting to your
> request. I'm not sure why that would be (No net neutrality rants, please).
>
> Anyway, if the credential check works even once then that is a good
> indication that the problem is outside ctakes.
>
> Sean
>
>
>
>
>
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Tuesday, February 27, 2018 7:49 AM
> To: dev@ctakes.apache.org
> Subject: RE: UmlsUserApprover Error [EXTERNAL]
>
> I guess you are running the build with test cases as I see the below
> messages in my case only while running build with test cases:
>
> >> log4j: reset attribute= "false".
> > > log4j: Threshold ="null".
> > > log4j: Retreiving an instance of org.apache.log4j.Logger.
> > > log4j: Setting [ProgressAppender] additivity to [false].
> > > log4j: Level value for ProgressAppender is [INFO].
> > > log4j: ProgressAppender level set to INFO
>
>
> Could you try building ' ctakes-temporal' module by skipping test case
> using the command - " mvn clean install -Dmaven.test.skip=true" ?
>
> Regards,
> Gandhi
>
> -Original Message-
> From: Andrew Phillips [mailto:aphilli...@luc.edu]
> Sent: Tuesday, February 27, 2018 7:08 AM
> To: dev@ctakes.apache.org
> Subject: Re: UmlsUserApprover Error [EXTERNAL]
>
> Thanks for the ideas.
>
> There hasn't been any such changes, and network connectivity shouldn't be
> an issue. I ran my script earlier, which automatically runs the same
> pipeline on several different folders, and only the first run was
> successful. The others failed with the same error. My latest attempt is to
> remove the .m2 directory and recompile and reinstall, and it is currently
> processing the first directory, so I don't know if it will fail on the next
> as yet.
>
> My primary interface is over SSH to a remote server, and this is the
> script:
> UmlsLP () { mvn exec:java
> -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
> -Dexec.args="--input-dir $1/yes/ --output-dir $2/yes/"
> -Dctakes.umlsuser= -Dctakes.umlspw= > out.tmp ; mvn exec:java
> -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
> -Dexec.args="--input-dir $1/no/ --output-dir $2/no/"
> -Dctakes.umlsuser= -Dctakes.umlspw= >> out.tmp ; echo Finished
> UmlsLP $1 $2 ; cat out.tmp | grep -C 3 "Total time" ;}
>
> Thank you.
>
>
> *Andrew Phillips*
> GitHub: github.com/skeledrew
> LinkedIn: www.linkedin.com/in/aphillipstech
>
> On 26 February 2018 at 13:00, Miller, Timothy < Timothy.Miller@childrens.
> harvard.edu> wrote:
>
> > Is it possible there is some network issue preventing connectivity?
> > New institutional firewall maybe?
> >
> > Otherwise, it looks like somehow your credentials are not getting into
> > the right place. Possible a configuration file had them before and
> > it's been changed out from under you?
> >
> > One thing you can try, if you are using an IDE, you can directly put
> > your credentials into the VM options for your run configuration with:
> > -Dctakes.uml
RE: UmlsUserApprover Error [EXTERNAL]
Hi Andrew,
You wrote:
> I ran my script earlier, [...]and only the first run was successful.
Are you saying that one run did succeed? If that is the case then the problem
probably is your network.
The umls credential check will print dots in the log as time progresses, such
as the dots from your log below:
> > 24 Feb 2018 18:22:25 INFO UmlsUserApprover - Checking UMLS Account
[ ... ]
> > .. 10
> > ...
> > 24 Feb 2018 18:22:40 ERROR UmlsUserApprover - uts-ws.nlm.nih.gov
It looks like the credential check took several (~15?) seconds, which might
indicate a slow connection or an eventual connection refused. That does not
mean that the slowdown is on your side. It could be that the nih server that
handles the credential checks is rarely getting to your request. I'm not sure
why that would be (No net neutrality rants, please).
Anyway, if the credential check works even once then that is a good indication
that the problem is outside ctakes.
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, February 27, 2018 7:49 AM
To: dev@ctakes.apache.org
Subject: RE: UmlsUserApprover Error [EXTERNAL]
I guess you are running the build with test cases as I see the below messages
in my case only while running build with test cases:
>> log4j: reset attribute= "false".
> > log4j: Threshold ="null".
> > log4j: Retreiving an instance of org.apache.log4j.Logger.
> > log4j: Setting [ProgressAppender] additivity to [false].
> > log4j: Level value for ProgressAppender is [INFO].
> > log4j: ProgressAppender level set to INFO
Could you try building ' ctakes-temporal' module by skipping test case using
the command - " mvn clean install -Dmaven.test.skip=true" ?
Regards,
Gandhi
-Original Message-
From: Andrew Phillips [mailto:aphilli...@luc.edu]
Sent: Tuesday, February 27, 2018 7:08 AM
To: dev@ctakes.apache.org
Subject: Re: UmlsUserApprover Error [EXTERNAL]
Thanks for the ideas.
There hasn't been any such changes, and network connectivity shouldn't be an
issue. I ran my script earlier, which automatically runs the same pipeline on
several different folders, and only the first run was successful. The others
failed with the same error. My latest attempt is to remove the .m2 directory
and recompile and reinstall, and it is currently processing the first
directory, so I don't know if it will fail on the next as yet.
My primary interface is over SSH to a remote server, and this is the script:
UmlsLP () { mvn exec:java
-Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
-Dexec.args="--input-dir $1/yes/ --output-dir $2/yes/"
-Dctakes.umlsuser= -Dctakes.umlspw= > out.tmp ; mvn exec:java
-Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
-Dexec.args="--input-dir $1/no/ --output-dir $2/no/"
-Dctakes.umlsuser= -Dctakes.umlspw= >> out.tmp ; echo Finished
UmlsLP $1 $2 ; cat out.tmp | grep -C 3 "Total time" ;}
Thank you.
*Andrew Phillips*
GitHub: github.com/skeledrew
LinkedIn: www.linkedin.com/in/aphillipstech
On 26 February 2018 at 13:00, Miller, Timothy <
timothy.mil...@childrens.harvard.edu> wrote:
> Is it possible there is some network issue preventing connectivity?
> New institutional firewall maybe?
>
> Otherwise, it looks like somehow your credentials are not getting into
> the right place. Possible a configuration file had them before and
> it's been changed out from under you?
>
> One thing you can try, if you are using an IDE, you can directly put
> your credentials into the VM options for your run configuration with:
> -Dctakes.umlsuser= -Dctakes.umlspw
>
> and see if you still get the issue.
>
> Tim
>
>
> On Sat, 2018-02-24 at 18:42 -0600, Andrew Phillips wrote:
> > Hello,
> >
> > I am getting an error after recompiling a script in my pipeline. My
> > setup was working fine the last time I did a compile several months
> > ago, and I have logged into my UMLS account to ensure it isn't an
> > issue with my credentials, as well as done a complete reinstall from
> > the GitHub repo and checked out the 4.0.0 release. The minor change
> > I made in the script was just uncommenting something that I've used
> > before, so I know there are no errors in it. Any insights as to what
> > the issue may be? I've included the complete output below. Thank
> > you.
> >
> >
> > [INFO] Scanning for projects...
> > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is
> > missing, no dependency information available [WARNING] Failed to
> > retrieve plugin descriptor for
> > org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin
>
RE: UmlsUserApprover Error [EXTERNAL]
I guess you are running the build with test cases as I see the below messages
in my case only while running build with test cases:
>> log4j: reset attribute= "false".
> > log4j: Threshold ="null".
> > log4j: Retreiving an instance of org.apache.log4j.Logger.
> > log4j: Setting [ProgressAppender] additivity to [false].
> > log4j: Level value for ProgressAppender is [INFO].
> > log4j: ProgressAppender level set to INFO
Could you try building ' ctakes-temporal' module by skipping test case using
the command - " mvn clean install -Dmaven.test.skip=true" ?
Regards,
Gandhi
-Original Message-
From: Andrew Phillips [mailto:aphilli...@luc.edu]
Sent: Tuesday, February 27, 2018 7:08 AM
To: dev@ctakes.apache.org
Subject: Re: UmlsUserApprover Error [EXTERNAL]
Thanks for the ideas.
There hasn't been any such changes, and network connectivity shouldn't be an
issue. I ran my script earlier, which automatically runs the same pipeline on
several different folders, and only the first run was successful. The others
failed with the same error. My latest attempt is to remove the .m2 directory
and recompile and reinstall, and it is currently processing the first
directory, so I don't know if it will fail on the next as yet.
My primary interface is over SSH to a remote server, and this is the script:
UmlsLP () { mvn exec:java
-Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
-Dexec.args="--input-dir $1/yes/ --output-dir $2/yes/"
-Dctakes.umlsuser= -Dctakes.umlspw= > out.tmp ; mvn exec:java
-Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
-Dexec.args="--input-dir $1/no/ --output-dir $2/no/"
-Dctakes.umlsuser= -Dctakes.umlspw= >> out.tmp ; echo Finished
UmlsLP $1 $2 ; cat out.tmp | grep -C 3 "Total time" ;}
Thank you.
*Andrew Phillips*
GitHub: github.com/skeledrew
LinkedIn: www.linkedin.com/in/aphillipstech
On 26 February 2018 at 13:00, Miller, Timothy <
timothy.mil...@childrens.harvard.edu> wrote:
> Is it possible there is some network issue preventing connectivity?
> New institutional firewall maybe?
>
> Otherwise, it looks like somehow your credentials are not getting into
> the right place. Possible a configuration file had them before and
> it's been changed out from under you?
>
> One thing you can try, if you are using an IDE, you can directly put
> your credentials into the VM options for your run configuration with:
> -Dctakes.umlsuser= -Dctakes.umlspw
>
> and see if you still get the issue.
>
> Tim
>
>
> On Sat, 2018-02-24 at 18:42 -0600, Andrew Phillips wrote:
> > Hello,
> >
> > I am getting an error after recompiling a script in my pipeline. My
> > setup was working fine the last time I did a compile several months
> > ago, and I have logged into my UMLS account to ensure it isn't an
> > issue with my credentials, as well as done a complete reinstall from
> > the GitHub repo and checked out the 4.0.0 release. The minor change
> > I made in the script was just uncommenting something that I've used
> > before, so I know there are no errors in it. Any insights as to what
> > the issue may be? I've included the complete output below. Thank
> > you.
> >
> >
> > [INFO] Scanning for projects...
> > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is
> > missing, no dependency information available [WARNING] Failed to
> > retrieve plugin descriptor for
> > org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin
> > org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies
> > could not be resolved: Failure to find
> > org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apac
> > h
> > e.org_maven2=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&
> > r
> > =Heup-IbsIg9Q1TPOylpP9FE4GTK-
> > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=NHws3pftXkncEWsu-
> > Y6fCtMKfY3WWkYQmDYrA4AVcvU=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh-
> > PSEuxpA= was cached in the local repository, resolution will not
> > be reattempted until the update interval of central has elapsed or
> > updates are forced [INFO] [INFO]
> > ---
> > -
> > [INFO] Building Apache cTAKES Temporal Information Extraction 4.0.1-
> > SNAPSHOT [INFO]
> > ---
> > -
> > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is
> > missing, no dependency information available [WARNING] Failed to
> > retrieve plugin descriptor for
> > org.eclipse.m2e:lifecycle-
Re: UmlsUserApprover Error [EXTERNAL]
Thanks for the ideas.
There hasn't been any such changes, and network connectivity shouldn't be
an issue. I ran my script earlier, which automatically runs the same
pipeline on several different folders, and only the first run was
successful. The others failed with the same error. My latest attempt is to
remove the .m2 directory and recompile and reinstall, and it is currently
processing the first directory, so I don't know if it will fail on the next
as yet.
My primary interface is over SSH to a remote server, and this is the script:
UmlsLP () { mvn exec:java
-Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
-Dexec.args="--input-dir $1/yes/ --output-dir $2/yes/"
-Dctakes.umlsuser= -Dctakes.umlspw= > out.tmp ; mvn exec:java
-Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
-Dexec.args="--input-dir $1/no/ --output-dir $2/no/"
-Dctakes.umlsuser= -Dctakes.umlspw= >> out.tmp ; echo Finished
UmlsLP $1 $2 ; cat out.tmp | grep -C 3 "Total time" ;}
Thank you.
*Andrew Phillips*
GitHub: github.com/skeledrew
LinkedIn: www.linkedin.com/in/aphillipstech
On 26 February 2018 at 13:00, Miller, Timothy <
timothy.mil...@childrens.harvard.edu> wrote:
> Is it possible there is some network issue preventing connectivity? New
> institutional firewall maybe?
>
> Otherwise, it looks like somehow your credentials are not getting into
> the right place. Possible a configuration file had them before and it's
> been changed out from under you?
>
> One thing you can try, if you are using an IDE, you can directly put
> your credentials into the VM options for your run configuration with:
> -Dctakes.umlsuser= -Dctakes.umlspw
>
> and see if you still get the issue.
>
> Tim
>
>
> On Sat, 2018-02-24 at 18:42 -0600, Andrew Phillips wrote:
> > Hello,
> >
> > I am getting an error after recompiling a script in my pipeline. My
> > setup
> > was working fine the last time I did a compile several months ago,
> > and I
> > have logged into my UMLS account to ensure it isn't an issue with my
> > credentials, as well as done a complete reinstall from the GitHub
> > repo and
> > checked out the 4.0.0 release. The minor change I made in the script
> > was
> > just uncommenting something that I've used before, so I know there
> > are no
> > errors in it. Any insights as to what the issue may be? I've included
> > the
> > complete output below. Thank you.
> >
> >
> > [INFO] Scanning for projects...
> > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is
> > missing, no dependency information available
> > [WARNING] Failed to retrieve plugin descriptor for
> > org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin
> > org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies
> > could
> > not be resolved: Failure to find
> > org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apach
> > e.org_maven2=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
> > =Heup-IbsIg9Q1TPOylpP9FE4GTK-
> > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=NHws3pftXkncEWsu-
> > Y6fCtMKfY3WWkYQmDYrA4AVcvU=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh-
> > PSEuxpA= was cached in the local repository,
> > resolution will not be reattempted until the update interval of
> > central has
> > elapsed or updates are forced
> > [INFO]
> > [INFO]
> > ---
> > -
> > [INFO] Building Apache cTAKES Temporal Information Extraction 4.0.1-
> > SNAPSHOT
> > [INFO]
> > ---
> > -
> > [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is
> > missing, no dependency information available
> > [WARNING] Failed to retrieve plugin descriptor for
> > org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin
> > org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies
> > could
> > not be resolved: Failure to find
> > org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apach
> > e.org_maven2=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
> > =Heup-IbsIg9Q1TPOylpP9FE4GTK-
> > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=NHws3pftXkncEWsu-
> > Y6fCtMKfY3WWkYQmDYrA4AVcvU=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh-
> > PSEuxpA= was cached in the local repository,
> > resolution will not be reattempted until the update interval of
> > central has
> > elapsed or updates are forced
> > [INFO]
> > [INFO] >>> exec-maven-plugin:1.2.1:java (default-cli) > validate @
> > ctakes-misc >>>
> > [INFO]
> > [INFO] <<< exec-maven-plugin:1.2.1:java (default-cli) < validate @
> > ctakes-misc <<<
> > [INFO]
> > [INFO]
> > [INFO] --- exec-maven-plugin:1.2.1:java (default-cli) @ ctakes-misc
> > ---
> > log4j: reset attribute= "false".
> > log4j: Threshold ="null".
> > log4j: Retreiving an instance of org.apache.log4j.Logger.
> > log4j: Setting [ProgressAppender] additivity to [false].
> > log4j: Level value for ProgressAppender is
Re: UmlsUserApprover Error [EXTERNAL]
Is it possible there is some network issue preventing connectivity? New
institutional firewall maybe?
Otherwise, it looks like somehow your credentials are not getting into
the right place. Possible a configuration file had them before and it's
been changed out from under you?
One thing you can try, if you are using an IDE, you can directly put
your credentials into the VM options for your run configuration with:
-Dctakes.umlsuser= -Dctakes.umlspw
and see if you still get the issue.
Tim
On Sat, 2018-02-24 at 18:42 -0600, Andrew Phillips wrote:
> Hello,
>
> I am getting an error after recompiling a script in my pipeline. My
> setup
> was working fine the last time I did a compile several months ago,
> and I
> have logged into my UMLS account to ensure it isn't an issue with my
> credentials, as well as done a complete reinstall from the GitHub
> repo and
> checked out the 4.0.0 release. The minor change I made in the script
> was
> just uncommenting something that I've used before, so I know there
> are no
> errors in it. Any insights as to what the issue may be? I've included
> the
> complete output below. Thank you.
>
>
> [INFO] Scanning for projects...
> [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is
> missing, no dependency information available
> [WARNING] Failed to retrieve plugin descriptor for
> org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin
> org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies
> could
> not be resolved: Failure to find
> org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in
> https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apach
> e.org_maven2=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
> =Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=NHws3pftXkncEWsu-
> Y6fCtMKfY3WWkYQmDYrA4AVcvU=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh-
> PSEuxpA= was cached in the local repository,
> resolution will not be reattempted until the update interval of
> central has
> elapsed or updates are forced
> [INFO]
> [INFO]
> ---
> -
> [INFO] Building Apache cTAKES Temporal Information Extraction 4.0.1-
> SNAPSHOT
> [INFO]
> ---
> -
> [WARNING] The POM for org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 is
> missing, no dependency information available
> [WARNING] Failed to retrieve plugin descriptor for
> org.eclipse.m2e:lifecycle-mapping:1.0.0: Plugin
> org.eclipse.m2e:lifecycle-mapping:1.0.0 or one of its dependencies
> could
> not be resolved: Failure to find
> org.eclipse.m2e:lifecycle-mapping:jar:1.0.0 in
> https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apach
> e.org_maven2=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
> =Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=NHws3pftXkncEWsu-
> Y6fCtMKfY3WWkYQmDYrA4AVcvU=1C-i1p8UnA38es-UT_d0FMIUOx5yrfK0NQh-
> PSEuxpA= was cached in the local repository,
> resolution will not be reattempted until the update interval of
> central has
> elapsed or updates are forced
> [INFO]
> [INFO] >>> exec-maven-plugin:1.2.1:java (default-cli) > validate @
> ctakes-misc >>>
> [INFO]
> [INFO] <<< exec-maven-plugin:1.2.1:java (default-cli) < validate @
> ctakes-misc <<<
> [INFO]
> [INFO]
> [INFO] --- exec-maven-plugin:1.2.1:java (default-cli) @ ctakes-misc
> ---
> log4j: reset attribute= "false".
> log4j: Threshold ="null".
> log4j: Retreiving an instance of org.apache.log4j.Logger.
> log4j: Setting [ProgressAppender] additivity to [false].
> log4j: Level value for ProgressAppender is [INFO].
> log4j: ProgressAppender level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%m].
> log4j: Adding appender named [noEolAppender] to category
> [ProgressAppender].
> log4j: Retreiving an instance of org.apache.log4j.Logger.
> log4j: Setting [ProgressDone] additivity to [false].
> log4j: Level value for ProgressDone is [INFO].
> log4j: ProgressDone level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%m%n].
> log4j: Adding appender named [eolAppender] to category
> [ProgressDone].
> log4j: Level value for root is [INFO].
> log4j: root level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%d{dd MMM
> HH:mm:ss}
> %5p %c{1} - %m%n].
> log4j: Adding appender named [consoleAppender] to category [root].
> 24 Feb 2018 18:22:23 INFO LvgAnnotator - URL for lvg.properties
> =/home/aphillips5/ctakes/ctakes-
> misc/target/classes/org/apache/ctakes/lvg/data/config/lvg.properties
> 24 Feb 2018 18:22:23 INFO SentenceDetector - Sentence
